Aplicación de la ingeniería del software sobre la herramienta MATE: Common y DMLib

Aquest projecte intenta implantar una metodologia de treball sobre MATE. MATE es una eina de sintonització d'aplicacions paral·leles sorgida de la tesis doctoral d'Anna Sikora a 2003. Vistos els resultats obtinguts, es va decidir donar un pas endavant i convertir-la en un producte software Open Source. Per fer-ho ha sigut necessari aplicar una serie d'estàndards i fer un proces de tests. En aquest treball s'ha creat part de la metodologia i s'han modificat dos dels mòduls principals.

Segregation in a mycorrhizal fungus alters rice growth and symbiosis-specific gene transcription

Arbuscular mycorrhizal fungi (AMF) form symbioses with the majority of plants, improving plant nutrition and diversity. Evidence exists suggesting that AMF contain populations of genetically different nucleotypes coexisting in a common cytoplasm. This potentially has two important consequences for their genetics. First, by random distribution of nuclei at spore formation, new offspring of an AMF could receive different complements of nucleotypes compared to the parent or siblings-we consider this as segregation. Second, genetic exchange between AMF would allow the mixing of nuclei, altering nucleotype diversity in new spores. Because segregation was assumed not to occur and genetic exchange has only recently been demonstrated, no attempts have been made to test whether this affects the symbiosis with plants. Here, we show that segregation occurs in the AMF Glomus intraradices and can enhance the growth of rice up to five times, even though neither parental nor crossed AMF lines induced a positive growth response. This process also resulted in an alteration of symbiosis-specific gene transcription in rice. Our results demonstrate that manipulation of AMF genetics has important consequences for the symbiotic effects on plants and could be used to enhance the growth of globally important crops.

Plasticity in sex allocation in the plant Mercurialis annua is greater for hermaphrodites sampled from dimorphic than from monomorphic populations.

Plants are notoriously variable in gender, ranging in sex allocation from purely male through hermaphrodite to purely female. This variation can have both a genetic and an adaptive plastic component. In gynodioecious species, where females co-occur with hermaphrodites, hermaphrodites tend to shift their allocation towards greater maleness when growing under low-resource conditions, either as a result of hermaphrodites shifting away from an expensive female function, or because of enhanced siring advantages in the presence of females. Similarly, in the androdioecious plant Mercurialis annua, where hermaphrodites co-exist with males, hermaphrodites also tend to enhance their relative male allocation under low-resource conditions. Here, we ask whether this response differs between hermaphrodites that have been evolving in the presence of males, in a situation analogous to that supposed for gynodioecious populations, vs. those that have been evolving in their absence. We grew hermaphrodites of M. annua from populations in which males were either present or absent under different levels of nutrient availability and compared their reaction norms. We found that, overall, hermaphrodites from populations with males tended to be more female than those from populations lacking males. Importantly, hermaphrodites' investment in pollen and seed production was more plastic when they came from populations with males than without them, reducing their pollen production at low resource availability and increasing their seed production at high resource availability. These results are consistent with the hypothesis that plasticity in sex allocation is enhanced in hermaphrodites that have likely been exposed to variation in mating opportunities due to fluctuations in the frequency of co-occurring males.

Biochemical characterization of a trypanosomatid isolated from the plant Amaranthus retroflexus

A protozoan flagelate has recently been isolated from Amaranthus retroflexus. This plant grows near economically important crops in southeastern Spain, which are known to be parasitized by Phytomonas spp. The present study focuses on the characterization of the energy metabolism of this new isolate. These flagellates utilize glucose efficiently as their primary energy source, although they are unable to completely degrade it. They excrete ethanol, acetate, glycine, and succinate in lower amount, as well as ammonium. The presence of glycosomes was indicated by the early enzymes of the glycolytic pathway, one enzyme of the glycerol pathway (glycerol kinase), and malate dehydrogenase. No evidence of a fully functional citric-acid cycle was found. In the absence of catalase activity, these flagellates showed significant superoxide dismutase activity located in the glycosomal and cytosolic fractions. These trypanosomes, despite being morphologically and metabolically similar to other Phytomonas isolated from the same area, showed significant differences, suggesting that they are phylogenetically different species.

The cuticle : not only a barrier for plant defence: A novel defence syndrome in plants with cuticular defects.

The cuticle is a physical barrier that prevents water loss and protects against irradiation, xenobiotics and pathogens. This classic textbook statement has recently been revisited and several observations were made showing that this dogma falls short of being universally true. Both transgenic Arabidopsis thaliana lines expressing cell wall-targeted fungal cutinase (so-called CUTE plants) or lipase as well as several A. thaliana mutants with altered cuticular structure remained free of symptoms after an inoculation with Botrytis cinerea. The alterations in cuticular structure lead to the release of fungitoxic substances and changes in gene expression that form a multifactorial defence response. Several models to explain this syndrome are discussed.

Registre isotòpic d'alquenones i lípids terrestres en sediment marí: una reconstrucció paleoclimàtica a l'oceà Índic

Projecte de recerca elaborat a partir d’una estada a la Institute of mineralogy and geochemistry de la University of Lausanne, Suïssa, entre 2007 i 2009. Durant l’última dècada, la comunitat científica ha reconegut que les zones tropicals juguen un paper clau en els processos dinàmics que controlen el canvi climàtic global, probablement com a desencadenant dels canvis succeïts en altes latituds. A més a més, els sediments dels oceans tropicals, en trobar-se fora de l’impacte directe de les plaques de gel continentals creades durant les glaciacions, proporcionen un registre continu de les variacions climàtiques del planeta. Malgrat tot, encara hi ha moltes incògnites sobre el paper específic de les zones tropicals, especialment pel que fa a les variacions brusques suborbitals, degut als pocs registres d’alta resolució estudiats en aquestes àrees que abastin varis cicles glacial/interglacial. Per tal d’ajudar a clarificar el paper de les zones tropicals de l’hemisferi sud en el control del clima a escala mil•lenària s’ha estudiat la distribució i la composició isotòpica de biomarcadors moleculars marins i terrestres, a baixa resolució, en el testimoni MD98-2165 (9º39’S, 118º20’E, 2100 m de profunditat d’aigua, 42.3 m de llarg) està situat al sud-oest d’Indonèsia, on s’enregistren les temperatures superficials del mar més elevades del planeta i una elevada activitat convectiva, que té una influència en la distribució de la humitat atmosfèrica en una extensa superfície de la Terra. Les distribucions observades de biomarcadors terrígens (C23-C33 n-alcans i C20-C32 n-alcan-1-ols) són típiques del lipids de plantes superiors que arriben a l’oceà principalment per via eòlica. L’alcà de 31 àtoms de carboni i els alcohols de 28 o 32 àtoms de carboni són els homòlegs més abundants en ambdós testimonis. Cal destacar l’alcohol C32 com a homòleg principal durant les èpoques glacials, tot suggerint una expansió de les plantes tropicals C4 associada a unes condicions més àrides. La procedència d’aquests lipids queda corroborada mitjançant la seva composició isotòpica de carboni, que ens permet diferenciar la ruta fotosintètica emprada i per tant, entre el tipus de plantes.

Bone anabolic potential of soy isoflavones and plant extracts and genomic changes during differentiation of hPOB-tert osteoblast-like cells

Summary For the nutritional management of bone health and the prevention of osteoporosis it is important to identify nutrients that positively influence the bone remodeling process at the cellular level. Soy isoflavones show promising osteoprotective effects in animals and humans but their mechanism of action in bone cells is yet poorly understood. Firstly, soy tissue cultures were characterized as a new and optimized source of isoflavones. A large variability in the isoflavone content was observed and high-producing strains (46.3 mg/g dry wt isoflavones) were identified. In the Ishikawa cells bioassay, the estrogenicity of isoflavones was confirmed to be 1000 to 10000 less than 17Mestradiol and that of the malonyl forms was shown for the first time (EC50 of 350 nM and 1880 nM for malonylgenistin and malonyldaidzin, respectively). The estrogenic activity of soya tissue culture extracts correlated to their isoflavone content. Secondly, the effects of phytonutrients on BMP-2 gene expression and on the mevalonate synthesis pathway, as key mediators of bone formation, were investigated. Dietary achievable concentrations of genistein and daidzein (10vM), and statins (4xM) but not 17M estradiol (10nM), induced BMP-2 gene expression (by up to 3-fold) and inhibited the cholesterol biosynthetic pathway (by up to 50%) in the human osteoblastic cell line hP0B¬tert. In addition, several plant extracts (Cyperus rotundus, Lindera benzoin and Cnidium monnieri) induced BMP-2 gene expression but this induction was not restricted to the inhibition of the cholesterol synthesis pathway neither to the estrogenicity. Finally, the gene expression profiles during hP0B-tert differentiation induced by vitamin D and dexamethasone were analyzed with the Affymetrix human GeneChip. 1665 different genes and 98 ESTs were significantly regulated. The expression profiles of bone-related genes was largely in agreement with previously documented patterns, supporting the physiological relevance of the genomic results and the hP0B-tert cell line as a valid model of human osteoblast differentiation. The expression of alternative differentiation markers during the osteogenic treatment of hP0B-tert cells indicated that the adipocyte and myoblast differentiation pathways were repressed, confirming that these culture conditions allowed only osteoblast differentiation. The gene ontology analysis identified further sub-groups of genes that may be involved in the bone formation process. Aims of the thesis In order to define new strategies for the nutritional management of bone health and for the prevention of osteoporosis the major goal of the present work was to investigate the potential of phytonutrients to positively modulate the bone formation process at the cellular level and, in particular: 1.To select and optimise alternative plant sources containing high levels of isoflavones with estrogenic activity (Chapter 3). 2.To compare the effects of statins and phytonutrients on BMP-2 gene expression and on the mevalonate synthesis pathway and to select new plant extracts with a bone anabolic potential (Chapter 4). 3.To further characterize the new human periosteal cell line, hP0B-tert, as a bone- formation model, by elucidating its gene expression profile during differentiation induced by vitamin D and dexamethasone (Chapter 5).

Gross Hemoglobinuria and Oliguria are Common Transient Complications of Sclerotherapy for Venous Malformations: Review of 475 Procedures.

Estudi retrospectiu per analitzar la incidència, factors de risc i tractament de la hemoglobinuria macroscòpica i oliguria després del tractament de malformacions venoses amb escleroteràpia. Un total de 475 procediments es van realitzar en 131 malalts usant etanol, sulfat tetradecil sòdic o ambdos. Hemoglobinuria temporal es va donar després del 34% de procediments i el 57% d’aquests es van asociar amb oliguria temporal. Aquest risc augmenta amb el increment de dosis. La resolució de la hemoglobinuria i oliguria va ser satisfactòria en tots els malalts. El risc d’hemoglobinuria augmenta a les malformacions que afecten les extremitats inferiors i a les de localitzacions mútiples.

Phytohormone collaboration: zooming in on auxin-brassinosteroid interactions.

Similar to animal hormones, classic plant hormones are small organic molecules that regulate physiological and developmental processes. In development, this often involves the regulation of growth through the control of cell size or division. The plant hormones auxin and brassinosteroid modulate both cell expansion and proliferation and are known for their overlapping activities in physiological assays. Recent molecular genetic analyses in the model plant Arabidopsis suggest that this reflects interdependent and often synergistic action of the two hormone pathways. Such pathway interactions probably occur through the combinatorial regulation of common target genes by auxin- and brassinosteroid-controlled transcription factors. Moreover, auxin and brassinosteroid signaling and biosynthesis and auxin transport might be linked by an emerging upstream connection involving calcium-calmodulin and phosphoinositide signaling.

Evaluating the ability of habitat suitability models to predict species presences.

Models predicting species spatial distribution are increasingly applied to wildlife management issues, emphasising the need for reliable methods to evaluate the accuracy of their predictions. As many available datasets (e.g. museums, herbariums, atlas) do not provide reliable information about species absences, several presence-only based analyses have been developed. However, methods to evaluate the accuracy of their predictions are few and have never been validated. The aim of this paper is to compare existing and new presenceonly evaluators to usual presence/absence measures. We use a reliable, diverse, presence/absence dataset of 114 plant species to test how common presence/absence indices (Kappa, MaxKappa, AUC, adjusted D-2) compare to presenceonly measures (AVI, CVI, Boyce index) for evaluating generalised linear models (GLM). Moreover we propose a new, threshold-independent evaluator, which we call "continuous Boyce index". All indices were implemented in the B10MAPPER software. We show that the presence-only evaluators are fairly correlated (p > 0.7) to the presence/absence ones. The Boyce indices are closer to AUC than to MaxKappa and are fairly insensitive to species prevalence. In addition, the Boyce indices provide predicted-toexpected ratio curves that offer further insights into the model quality: robustness, habitat suitability resolution and deviation from randomness. This information helps reclassifying predicted maps into meaningful habitat suitability classes. The continuous Boyce index is thus both a complement to usual evaluation of presence/absence models and a reliable measure of presence-only based predictions.

Polygodial, the fungitoxic component from the Brazilian medicinal plant Polygonum punctatum

Polygonum punctatum (Polygonaceae) is an herb known in some regions of Brazil as "erva-de-bicho" and is used to treat intestinal disorders. The dichloromethane extract of the aerial parts of this plant showed strong activity in a bioautographic assay with the fungus Cladosporium sphaerospermum. The bioassay-guided chemical fractionation of this extract afforded the sesquiterpene dialdehyde polygodial as the active constituent. The presence of this compound with antibiotic, anti-inflammatory and anti-hyperalgesic properties in "erva-de-bicho" may account for the effects attributed by folk medicine to this plant species.

Ablation of caterpillar labial salivary glands: technique for determining the role of saliva in insect-plant interactions.

There has been an ardent interest in herbivore saliva due to its roles in inducing plant defenses and its impact on herbivore fitness. Two techniques are described that inhibit the secretion of labial saliva from the caterpillar, Helicoverpa zea, during feeding. The methods rely on cauterizing the caterpillar's spinneret, the principal secretory structure of the labial glands, or surgically removing the labial salivary gland. Both methods successfully inhibit secretion of saliva and the principal salivary enzyme glucose oxidase. Caterpillars with inhibited saliva production feed at similar rates as the untreated caterpillars, pupate, and emerge as adults. Glucose oxidase has been suggested to increase the caterpillar's survival through the suppression of inducible anti-herbivore defenses in plants. Tobacco (Nicotiana tabacum) leaves fed on by caterpillars with ablated salivary glands had significantly higher levels of nicotine, an inducible anti-herbivore defense compound of tobacco, than leaves fed upon by caterpillars with intact labial salivary glands. Tomato (Lycopersicon esculentum) leaves fed upon by caterpillars with suppressed salivary secretions showed greatly reduced evidence of hydrogen peroxide formation compared to leaves fed upon by intact caterpillars. These two methods are useful techniques for determining the role that saliva plays in manipulating plant anti-herbivore defenses.

Immunodéficience commune variable: ce qu'il faut savoir [Common variable immune deficiency: what you need to know].

Common variable immune deficiency is the most frequent primary immune deficiency, characterized mainly by a disorder of B lymphocytes differentiation and a deficit in immunoglobulins. The clinical manifestations include recurrent infections, non-infectious lung and digestive involvements, autoimmune diseases, and an increased susceptibility to cancers. Recent breakthroughs have been made in the understanding of some genetic mechanisms of the disease. Replacement therapy with intravenous immunoglobulins remains the treatment of choice, which allows significant improvement in the survival and quality of life. However progress should be made in the understanding of the pathophysiology and in the early detection of this disease, since a delay in the diagnosis may have harmful consequences in terms of morbidity and mortality.

Thermogenic effects of commercially available plant preparations aimed at treating human obesity.

Different commercially available plant preparations have been claimed to have anti-obesity action. We investigated the acute effects of oral administration of 12 of these preparations in non-obese women and men. No significant increase in energy expenditure (EE) has been noted after treatment with any of these preparations. No change in respiratory quotient (RQ) was shown, except after treatment with maté (Ilex paraguariensis) extract, where a drop in RQ was observed, indicating a rise in the proportion of fat oxidized. The results suggested the poor potential of these plant preparations in the treatment of obesity, except possibly for the maté extract. Further studies are required to explore the influence of higher dosages of these preparations as well as chronic administration in man.

Cytotoxic and Antiviral Activities of Colombian Medicinal Plant Extracts of the Euphorbia genus

Forty-seven plant extracts of 10 species of the genus Euphorbia (Euphorbiaceae) used by Colombian traditional healers for the treatment of ulcers, cancers, tumors, warts, and other diseases, were tested in vitro for their potential antitumour (antiproliferative and cytotoxic) and antiherpetic activity. To evaluate the capacity of the extracts to inhibit the lytic activity of herpes simplex virus type 2 (HSV-2) and the reduction of viability of infected or uninfected cell cultures, the end-point titration technique (EPTT) and the MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] colorimetric assay were used, respectively. The therapeutic index of the positive extracts for the antiviral activity was determined by calculating the ratio CC50 (50% cytotoxic concentration) over IC50 (50% inhibitory concentration of the viral effect). Five of the 47 extracts (11%) representing 3 out of 10 Euphorbia species (30%) exhibited antiherpetic action; the highest activity was found in the leaf/stem water-methanol extracts from E. cotinifolia and E. tirucalli. The therapeutic indexes of these two plant species were > 7.1; these extracts exhibited no cytotoxicity. Six extracts (13%) representing 4 plant species (40%) showed cytotoxic activity. The highest cytotoxicity was found in the dichloromethane extract obtained from E. cotinifolia leaves and the CC50 values for the most susceptible cell lines, HEp-2 and CHO, were 35.1 and 18.1 µg/ml, respectively.